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1 <tool id="pieplots_macs" name="Pieplots MACS" version="0.1">
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2 <description>
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3 Peaks are assigned to the closest gene and then categorized according to their location at different genomic regions (promoter, intron, exon, or after the gene). Sites >10kb away from any gene are considered intergenic.
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4 </description>
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5 <parallelism method="basic"></parallelism>
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6 <requirements>
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7 <requirement type="package" version="0.14.1">pandas</requirement>
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8 <requirement type="package" version="1.4">matplotlib</requirement>
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9 </requirements>
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10 <command interpreter="python">
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11 pieplots_macs.py --genefile $genefile --peakfile $peakfile $MACS --outfile $out
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12 </command>
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13 <inputs>
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14 <param name="genefile" type="data" label="Gene file (map_peaks_to_genes)" help="" optional="false" />
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15 <param name="peakfile" type="data" label="Peaks file (narrowpeaks)" help="" optional="false" />
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16 <param name="MACS" checked="false" label="Set this value if you have MACS peaks" type="boolean" truevalue="--MACS" falsevalue="" help="" />
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17 </inputs>
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18 <outputs>
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19 <data name="out" format="pdf" hidden="false" />
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20 </outputs>
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21 <help></help>
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22 </tool>
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